Condoleezza Rice voiced “deep regret” today for a US Marine’s alleged rape of a 14-year-old Japanese girl, a case that has sparked outrage and official condemnation in Japan.

But the US Secretary of State insisted US-Japanese relations would recover, despite the angry backlash in the country.

Tyrone Hadnott, 38, has been arrested on suspicion of raping the girl in a car on Okinawa island, where the bulk of the 50,000 US troops in Japan are based.

Police have said he denied rape but admitted forcing her to kiss him.

The incident has revived bitter memories of the rape of a 12-year-old schoolgirl on the southern Japanese island in 1995, which sparked huge protests against US bases and raised doubts about the bilateral security alliance.

At the start of a one-day trip to Japan, Rice said: “We just regret deeply that this happened. It is very hard to see something like this happen and it’s especially hard because it involves a young girl.”

Japanese Prime Minister Yasuo Fukuda has called the latest incident “unforgivable” and demanded tighter military discipline.

Asked if the case might harm the US-Japanese alliance, Rice replied: “We certainly hope that there will not be lasting effects. It’s a long-standing and strong alliance.

“But our concern right now is to see that justice is done, to get to the bottom of it, and our concern is for the girl and for her family.”

In a meeting with Rice, Japan’s Defence Minister Shigeru Ishiba underlined the gravity of the incident, which comes amid a struggle to implement a plan lightening the burden of the US military presence on Okinawa following the 1995 incident.

Ishibia told Rice: “Okinawa is very important, not only for Japan, but for the United States.

“From that point of view, the incident in Okinawa is very unfortunate, and it is also unfortunate for the bilateral alliance between our countries.”

Rice was visiting Japan after attending the inauguration of South Korean President Lee Myung-bak in Seoul on Monday and discussing how to end North Korea’s nuclear programmes with Chinese officials in Beijing yesterday.